fixing bug in findcandidatebyexamplesvc (#5101)
* fixing build * cleanup * review fix * review changes --------- Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
This commit is contained in:
TipzCM
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d6fae7c673
commit
cf8c70994f
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@ -0,0 +1,7 @@
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---
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type: fix
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issue: 5100
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title: "Fixed a bug in FindCandidateByExampleSvc that resulted in
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class cast exceptions for IResourcePersistentIds that are not
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based on Long value ids.
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"
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@ -93,7 +93,7 @@ public class FindCandidateByExampleSvc<P extends IResourcePersistentId> extends
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// we'll track the added ids so we don't add the same resources twice
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// note, all these resources are the same type, so we only need the Long value
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Set<Long> currentIds = new HashSet<>();
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Set<String> currentIds = new HashSet<>();
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for (MatchedTarget match : matchedCandidates) {
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Optional<? extends IMdmLink> optionalMdmLink = myMdmLinkDaoSvc.getMatchedLinkForSourcePid(
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myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), match.getTarget()));
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@ -125,7 +125,11 @@ public class FindCandidateByExampleSvc<P extends IResourcePersistentId> extends
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}
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// only add if it's not already in the list
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if (currentIds.add((Long) candidate.getCandidateGoldenResourcePid().getId())) {
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// NB: we cannot use hash of IResourcePersistentId because
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// BaseResourcePersistentId overrides this (and so is the same
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// for any class with the same version) :(
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if (currentIds.add(
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String.valueOf(candidate.getCandidateGoldenResourcePid().getId()))) {
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retval.add(candidate);
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}
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}
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@ -0,0 +1,26 @@
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package ca.uhn.fhir.jpa.mdm.helper.testmodels;
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import ca.uhn.fhir.rest.api.server.storage.BaseResourcePersistentId;
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/**
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* A test ResourceId with a non-long implementation of the id
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*/
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public class StringResourceId extends BaseResourcePersistentId<String> {
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private final String myId;
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public StringResourceId(String theId) {
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super(null);
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myId = theId;
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}
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public StringResourceId(Long theVersion, String theId) {
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super(theVersion, null);
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myId = theId;
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}
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@Override
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public String getId() {
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return myId;
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}
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}
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@ -0,0 +1,184 @@
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package ca.uhn.fhir.jpa.mdm.helper.testmodels;
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import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
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import ca.uhn.fhir.mdm.api.IMdmLink;
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import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
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import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
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import java.util.Date;
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public class TestMdmLink implements IMdmLink<StringResourceId> {
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private StringResourceId myId;
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private StringResourceId myGoldenResourceId;
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private StringResourceId mySourceResourceId;
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private MdmMatchResultEnum myMatchResultEnum;
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private MdmLinkSourceEnum myLinkSourceEnum;
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@Override
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public StringResourceId getId() {
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return myId;
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}
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@Override
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public IMdmLink<StringResourceId> setId(StringResourceId theId) {
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myId = theId;
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return this;
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}
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@Override
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public StringResourceId getGoldenResourcePersistenceId() {
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return myGoldenResourceId;
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}
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@Override
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public IMdmLink<StringResourceId> setGoldenResourcePersistenceId(StringResourceId theGoldenResourcePid) {
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myGoldenResourceId = theGoldenResourcePid;
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return this;
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}
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@Override
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public StringResourceId getSourcePersistenceId() {
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return mySourceResourceId;
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}
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@Override
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public IMdmLink<StringResourceId> setSourcePersistenceId(StringResourceId theSourcePid) {
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mySourceResourceId = theSourcePid;
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return this;
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}
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@Override
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public MdmMatchResultEnum getMatchResult() {
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return myMatchResultEnum;
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}
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@Override
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public IMdmLink<StringResourceId> setMatchResult(MdmMatchResultEnum theMatchResult) {
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myMatchResultEnum = theMatchResult;
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return this;
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}
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@Override
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public MdmLinkSourceEnum getLinkSource() {
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return myLinkSourceEnum;
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}
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@Override
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public IMdmLink<StringResourceId> setLinkSource(MdmLinkSourceEnum theLinkSource) {
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myLinkSourceEnum = theLinkSource;
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return this;
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}
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@Override
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public Date getCreated() {
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return new Date();
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}
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@Override
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public IMdmLink<StringResourceId> setCreated(Date theCreated) {
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// unneeded
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return this;
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}
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@Override
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public Date getUpdated() {
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return new Date();
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}
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@Override
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public IMdmLink<StringResourceId> setUpdated(Date theUpdated) {
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// unneeded
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return this;
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}
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@Override
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public String getVersion() {
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return null;
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}
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@Override
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public IMdmLink<StringResourceId> setVersion(String theVersion) {
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// unneeded
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return this;
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}
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@Override
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public Boolean getEidMatch() {
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return null;
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}
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@Override
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public Boolean isEidMatchPresent() {
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return null;
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}
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@Override
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public IMdmLink<StringResourceId> setEidMatch(Boolean theEidMatch) {
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return this;
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}
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@Override
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public Boolean getHadToCreateNewGoldenResource() {
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return null;
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}
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@Override
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public IMdmLink<StringResourceId> setHadToCreateNewGoldenResource(Boolean theHadToCreateNewGoldenResource) {
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return this;
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}
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@Override
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public Long getVector() {
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return null;
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}
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@Override
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public IMdmLink<StringResourceId> setVector(Long theVector) {
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return this;
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}
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@Override
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public Double getScore() {
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return null;
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}
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@Override
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public IMdmLink<StringResourceId> setScore(Double theScore) {
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return this;
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}
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@Override
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public Long getRuleCount() {
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return null;
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}
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@Override
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public IMdmLink<StringResourceId> setRuleCount(Long theRuleCount) {
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return this;
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}
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@Override
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public String getMdmSourceType() {
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return null;
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}
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@Override
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public IMdmLink<StringResourceId> setMdmSourceType(String theMdmSourceType) {
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return this;
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}
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@Override
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public void setPartitionId(PartitionablePartitionId thePartitionablePartitionId) {
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}
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@Override
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public PartitionablePartitionId getPartitionId() {
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return null;
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}
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}
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@ -0,0 +1,139 @@
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package ca.uhn.fhir.jpa.mdm.svc.candidate;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.interceptor.model.RequestPartitionId;
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import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
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import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
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import ca.uhn.fhir.jpa.mdm.helper.testmodels.StringResourceId;
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import ca.uhn.fhir.jpa.mdm.helper.testmodels.TestMdmLink;
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import ca.uhn.fhir.mdm.api.IMdmLink;
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import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
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import ca.uhn.fhir.mdm.api.MatchedTarget;
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import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
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import ca.uhn.fhir.mdm.util.MdmPartitionHelper;
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import org.hl7.fhir.r4.model.Patient;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.InjectMocks;
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import org.mockito.Mock;
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import org.mockito.Spy;
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import org.mockito.junit.jupiter.MockitoExtension;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Optional;
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import java.util.Set;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.ArgumentMatchers.anyString;
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import static org.mockito.Mockito.when;
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@ExtendWith(MockitoExtension.class)
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public class FindCandidateByExampleSvcTest {
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@Spy
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private FhirContext myFhirContext = FhirContext.forR4Cached();
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@Mock
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private IIdHelperService<StringResourceId> myIdHelperService;
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@Mock
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private MdmLinkDaoSvc<StringResourceId, IMdmLink<StringResourceId>> myMdmLinkDaoSvc;
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@Mock
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private MdmPartitionHelper myMdmPartitionHelper;
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@Mock
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private IMdmMatchFinderSvc myMdmMatchFinderSvc;
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@InjectMocks
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private FindCandidateByExampleSvc<StringResourceId> myFindCandidateByExampleSvc;
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@Test
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public void findMatchGoldenResourceCandidates_withNonLongIds_returnsList() {
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// setup
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int total = 3;
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Patient patient = new Patient();
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patient.setActive(true);
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patient.addName()
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.setFamily("Simpson")
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.addGiven("Homer");
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List<MatchedTarget> matchCandidatesList = new ArrayList<>();
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Map<String, Patient> targets = new HashMap<>();
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for (int i = 0; i < total*2; i++) {
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String id = "Test-" + (i % 3);
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if (!targets.containsKey(id)) {
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// the different names don't matter for the test
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// but makes debugging easier
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String name;
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if (i == 0) {
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name = "Bart";
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} else if (i == 1) {
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name = "Lisa";
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} else {
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name = "Maggie";
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}
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Patient p = new Patient();
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p.setActive(true);
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p.addName()
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.setFamily("Simpson")
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.addGiven(name);
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targets.put(id, p);
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}
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matchCandidatesList.add(
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new MatchedTarget(targets.get(id), MdmMatchOutcome.POSSIBLE_MATCH)
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);
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}
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// when
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when(myMdmPartitionHelper.getRequestPartitionIdFromResourceForSearch(any()))
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.thenReturn(RequestPartitionId.allPartitions());
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when(myIdHelperService.getPidOrNull(any(), any()))
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.thenReturn(new StringResourceId("omit"));
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when(myMdmLinkDaoSvc.getMdmLinksBySourcePidAndMatchResult(any(), any()))
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.thenReturn(new ArrayList<>());
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when(myMdmMatchFinderSvc.getMatchedTargets(anyString(), any(Patient.class), any()))
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.thenReturn(matchCandidatesList);
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// we don't care about the id we return here
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// because we are going to mock the return value anyways
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when(myIdHelperService.getPidOrNull(any(), any(Patient.class)))
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.thenReturn(new StringResourceId("test"));
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int[] count = new int[] { 0 };
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when(myMdmLinkDaoSvc.getMatchedLinkForSourcePid(any(StringResourceId.class)))
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.thenAnswer(args -> {
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if (count[0] < total) {
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TestMdmLink link = new TestMdmLink();
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link.setSourcePersistenceId(args.getArgument(0));
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if (count[0] % 2 == 0) {
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link.setGoldenResourcePersistenceId(new StringResourceId("even"));
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} else {
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link.setGoldenResourcePersistenceId(new StringResourceId("odd"));
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}
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count[0]++;
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return Optional.of(link);
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}
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return Optional.empty();
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});
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// test
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List<MatchedGoldenResourceCandidate> goldenResourceCanddiates = myFindCandidateByExampleSvc.findMatchGoldenResourceCandidates(patient);
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// verify
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assertNotNull(goldenResourceCanddiates);
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assertEquals(2, goldenResourceCanddiates.size());
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Set<String> ids = new HashSet<>();
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for (MatchedGoldenResourceCandidate r : goldenResourceCanddiates) {
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// we know these are strings
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assertTrue(ids.add((String)r.getCandidateGoldenResourcePid().getId()));
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}
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}
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}
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@ -0,0 +1,157 @@
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package ca.uhn.fhir.jpa.mdm.svc.candidate;
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import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
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import ca.uhn.fhir.jpa.entity.MdmLink;
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import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
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import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
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import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
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import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
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import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
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import org.hl7.fhir.r4.model.Patient;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.junit.jupiter.MockitoExtension;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.test.context.TestPropertySource;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.hasSize;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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@ExtendWith(MockitoExtension.class)
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@TestPropertySource(properties = {
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"module.mdm.config.script.file=classpath:mdm/mdm-rules-john-doe.json"
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})
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class MdmGoldenResourceFindingSvcIT extends BaseMdmR4Test {
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@Autowired
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MdmGoldenResourceFindingSvc myMdmGoldenResourceFindingSvc = new MdmGoldenResourceFindingSvc();
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@Autowired
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MdmLinkDaoSvc myMdmLinkDaoSvc;
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@Test
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public void testNoMatchCandidatesSkipped() {
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// setup
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Patient jane = createPatientAndUpdateLinks(addExternalEID(buildJanePatient(), EID_1));
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// hack the link into a NO_MATCH
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List<MdmLink> links = (List<MdmLink>) myMdmLinkDaoSvc.findMdmLinksBySourceResource(jane);
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assertThat(links, hasSize(1));
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MdmLink link = links.get(0);
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link.setMatchResult(MdmMatchResultEnum.NO_MATCH);
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link.setLinkSource(MdmLinkSourceEnum.MANUAL);
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myMdmLinkDaoSvc.save(link);
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// the NO_MATCH golden resource should not be a candidate
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CandidateList candidateList = myMdmGoldenResourceFindingSvc.findGoldenResourceCandidates(jane);
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assertEquals(0, candidateList.size());
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}
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@Test
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public void findMdmLinksBySourceResource_withMatchingResources_doesNotReturnDuplicates() {
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// setup
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// create a bunch of patients that match
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// (according to the rules in mdm-rules-john-doe.json)
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// patient 1
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{
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String patientStr = """
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{
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"resourceType": "Patient",
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"name": [ {
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"family": "Jho",
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"given": [ "Doe"]
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} ],
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"birthDate": "1974-12-25"
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}
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""";
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createPatientFromJsonString(patientStr, true);
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}
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// patient 2
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{
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String patientStr = """
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{
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"resourceType": "Patient",
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"name": [ {
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"family": "Jhyee",
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"given": [ "Deeon"]
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} ],
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"birthDate": "1974-12-25"
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}
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""";
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createPatientFromJsonString(patientStr, true);
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}
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// patient 3
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{
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String patientStr = """
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{
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"resourceType": "Patient",
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"name": [ {
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"family": "Jhoye",
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"given": [ "Deo"]
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} ],
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"birthDate": "1974-12-25"
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}
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""";
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createPatientFromJsonString(patientStr, true);
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}
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// patient 4
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{
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String patientStr = """
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{
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"resourceType": "Patient",
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"name": [ {
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"family": "Jhee",
|
||||
"given": [ "Deo"]
|
||||
} ],
|
||||
"birthDate": "1974-12-25"
|
||||
}
|
||||
""";
|
||||
createPatientFromJsonString(patientStr, true);
|
||||
}
|
||||
// patient 5
|
||||
Patient candidate;
|
||||
{
|
||||
String patientStr = """
|
||||
{
|
||||
"resourceType": "Patient",
|
||||
"name": [ {
|
||||
"family": "Jhee",
|
||||
"given": [ "Doe"]
|
||||
} ],
|
||||
"birthDate": "1974-12-25"
|
||||
}
|
||||
""";
|
||||
candidate = createPatientFromJsonString(patientStr, true);
|
||||
}
|
||||
|
||||
// test
|
||||
CandidateList candidateList = myMdmGoldenResourceFindingSvc.findGoldenResourceCandidates(candidate);
|
||||
|
||||
// verify
|
||||
assertNotNull(candidateList);
|
||||
Set<Long> ids = new HashSet<>();
|
||||
for (MatchedGoldenResourceCandidate c : candidateList.getCandidates()) {
|
||||
assertTrue(ids.add((Long) c.getCandidateGoldenResourcePid().getId()));
|
||||
}
|
||||
}
|
||||
|
||||
private Patient createPatientFromJsonString(String theStr, boolean theCreateGolden) {
|
||||
Patient patient = (Patient) myFhirContext.newJsonParser().parseResource(theStr);
|
||||
DaoMethodOutcome daoOutcome = myPatientDao.create(
|
||||
patient,
|
||||
new SystemRequestDetails()
|
||||
);
|
||||
|
||||
if (theCreateGolden) {
|
||||
myMdmMatchLinkSvc.updateMdmLinksForMdmSource(patient, createContextForCreate("Patient"));
|
||||
}
|
||||
|
||||
return (Patient) daoOutcome.getResource();
|
||||
}
|
||||
}
|
||||
|
|
@ -1,163 +0,0 @@
|
|||
package ca.uhn.fhir.jpa.mdm.svc.candidate;
|
||||
|
||||
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
|
||||
import ca.uhn.fhir.jpa.entity.MdmLink;
|
||||
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
|
||||
import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
|
||||
import ca.uhn.fhir.mdm.api.IMdmSettings;
|
||||
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
|
||||
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
|
||||
import ca.uhn.fhir.mdm.rules.json.MdmRulesJson;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import ca.uhn.fhir.test.utilities.UnregisterScheduledProcessor;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.test.context.ContextConfiguration;
|
||||
import org.springframework.test.context.TestPropertySource;
|
||||
import org.testcontainers.shaded.com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.hasSize;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
@TestPropertySource(properties = {
|
||||
"module.mdm.config.script.file=classpath:mdm/mdm-rules-john-doe.json"
|
||||
})
|
||||
class MdmGoldenResourceFindingSvcTest extends BaseMdmR4Test {
|
||||
|
||||
@Autowired
|
||||
MdmGoldenResourceFindingSvc myMdmGoldenResourceFindingSvc = new MdmGoldenResourceFindingSvc();
|
||||
@Autowired
|
||||
MdmLinkDaoSvc myMdmLinkDaoSvc;
|
||||
|
||||
@Test
|
||||
public void testNoMatchCandidatesSkipped() {
|
||||
// setup
|
||||
Patient jane = createPatientAndUpdateLinks(addExternalEID(buildJanePatient(), EID_1));
|
||||
|
||||
// hack the link into a NO_MATCH
|
||||
List<MdmLink> links = (List<MdmLink>) myMdmLinkDaoSvc.findMdmLinksBySourceResource(jane);
|
||||
assertThat(links, hasSize(1));
|
||||
MdmLink link = links.get(0);
|
||||
link.setMatchResult(MdmMatchResultEnum.NO_MATCH);
|
||||
link.setLinkSource(MdmLinkSourceEnum.MANUAL);
|
||||
myMdmLinkDaoSvc.save(link);
|
||||
|
||||
// the NO_MATCH golden resource should not be a candidate
|
||||
CandidateList candidateList = myMdmGoldenResourceFindingSvc.findGoldenResourceCandidates(jane);
|
||||
assertEquals(0, candidateList.size());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void findMdmLinksBySourceResource_withMatchingResources_doesNotReturnDuplicates() throws IOException {
|
||||
// setup
|
||||
// create a bunch of patients that match
|
||||
// (according to the rules in mdm-rules-john-doe.json)
|
||||
// patient 1
|
||||
{
|
||||
String patientStr = """
|
||||
{
|
||||
"resourceType": "Patient",
|
||||
"name": [ {
|
||||
"family": "Jho",
|
||||
"given": [ "Doe"]
|
||||
} ],
|
||||
"birthDate": "1974-12-25"
|
||||
}
|
||||
""";
|
||||
createPatientFromJsonString(patientStr, true);
|
||||
}
|
||||
// patient 2
|
||||
{
|
||||
String patientStr = """
|
||||
{
|
||||
"resourceType": "Patient",
|
||||
"name": [ {
|
||||
"family": "Jhyee",
|
||||
"given": [ "Deeon"]
|
||||
} ],
|
||||
"birthDate": "1974-12-25"
|
||||
}
|
||||
""";
|
||||
createPatientFromJsonString(patientStr, true);
|
||||
}
|
||||
// patient 3
|
||||
{
|
||||
String patientStr = """
|
||||
{
|
||||
"resourceType": "Patient",
|
||||
"name": [ {
|
||||
"family": "Jhoye",
|
||||
"given": [ "Deo"]
|
||||
} ],
|
||||
"birthDate": "1974-12-25"
|
||||
}
|
||||
""";
|
||||
createPatientFromJsonString(patientStr, true);
|
||||
}
|
||||
// patient 4
|
||||
{
|
||||
String patientStr = """
|
||||
{
|
||||
"resourceType": "Patient",
|
||||
"name": [ {
|
||||
"family": "Jhee",
|
||||
"given": [ "Deo"]
|
||||
} ],
|
||||
"birthDate": "1974-12-25"
|
||||
}
|
||||
""";
|
||||
createPatientFromJsonString(patientStr, true);
|
||||
}
|
||||
// patient 5
|
||||
Patient candidate;
|
||||
{
|
||||
String patientStr = """
|
||||
{
|
||||
"resourceType": "Patient",
|
||||
"name": [ {
|
||||
"family": "Jhee",
|
||||
"given": [ "Doe"]
|
||||
} ],
|
||||
"birthDate": "1974-12-25"
|
||||
}
|
||||
""";
|
||||
candidate = createPatientFromJsonString(patientStr, true);
|
||||
}
|
||||
|
||||
// test
|
||||
CandidateList candidateList = myMdmGoldenResourceFindingSvc.findGoldenResourceCandidates(candidate);
|
||||
|
||||
// verify
|
||||
assertNotNull(candidateList);
|
||||
Set<Long> ids = new HashSet<>();
|
||||
for (MatchedGoldenResourceCandidate c : candidateList.getCandidates()) {
|
||||
assertTrue(ids.add((Long)c.getCandidateGoldenResourcePid().getId()));
|
||||
}
|
||||
}
|
||||
|
||||
private Patient createPatientFromJsonString(String theStr, boolean theCreateGolden) {
|
||||
Patient patient = (Patient) myFhirContext.newJsonParser().parseResource(theStr);
|
||||
DaoMethodOutcome daoOutcome = myPatientDao.create(patient, new SystemRequestDetails());
|
||||
|
||||
if (theCreateGolden) {
|
||||
myMdmMatchLinkSvc.updateMdmLinksForMdmSource(patient, createContextForCreate("Patient"));
|
||||
}
|
||||
|
||||
return (Patient) daoOutcome.getResource();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -66,6 +66,9 @@ public class PointcutLatchSession {
|
|||
|
||||
List<HookParams> awaitExpectedWithTimeout(int theTimeoutSecond) throws InterruptedException {
|
||||
if (!myCountdownLatch.await(theTimeoutSecond, TimeUnit.SECONDS)) {
|
||||
if (!myFailures.isEmpty()) {
|
||||
ourLog.error(String.join(",", myFailures));
|
||||
}
|
||||
throw new LatchTimedOutError(Msg.code(1483) + myName + " timed out waiting " + theTimeoutSecond + " seconds for latch to countdown from " + myInitialCount + " to 0. Is " + myCountdownLatch.getCount() + ".");
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue